8BBW

Crystal structure of medical leech destabilase (low salt)

Summary for 8BBW

• Entry DOI: 10.2210/pdb8bbw/pdb
• Descriptor: Lysozyme, GLYCEROL, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: lysozyme, muramidase, isopeptidase, glycosidase, antibacterial, hydrolase
• Biological source: Hirudo medicinalis (medicinal leech)
• Total number of polymer chains: 1
• Total formula weight: 13952.79

Authors

Marin, E.,Bukhdruker, S.,Manuvera, V.,Kornilov, D.,Zinovev, E.,Bobrovsky, P.,Lazarev, V.,Borshchevskiy, V. (deposition date: 2022-10-14, release date: 2023-02-08, Last modification date: 2024-10-23)

Primary citation

Marin, E.,Kornilov, D.A.,Bukhdruker, S.S.,Aleksenko, V.A.,Manuvera, V.A.,Zinovev, E.V.,Kovalev, K.V.,Shevtsov, M.B.,Talyzina, A.A.,Bobrovsky, P.A.,Kuzmichev, P.K.,Mishin, A.V.,Gushchin, I.Y.,Lazarev, V.N.,Borshchevskiy, V.I.
Structural insights into thrombolytic activity of destabilase from medicinal leech.
Sci Rep, 13:6641-6641, 2023

PubMed Abstract: Destabilase from the medical leech Hirudo medicinalis belongs to the family of i-type lysozymes. It has two different enzymatic activities: microbial cell walls destruction (muramidase activity), and dissolution of the stabilized fibrin (isopeptidase activity). Both activities are known to be inhibited by sodium chloride at near physiological concentrations, but the structural basis remains unknown. Here we present two crystal structures of destabilase, including a 1.1 Å-resolution structure in complex with sodium ion. Our structures reveal the location of sodium ion between Glu34/Asp46 residues, which were previously recognized as a glycosidase active site. While sodium coordination with these amino acids may explain inhibition of the muramidase activity, its influence on previously suggested Ser49/Lys58 isopeptidase activity dyad is unclear. We revise the Ser49/Lys58 hypothesis and compare sequences of i-type lysozymes with confirmed destabilase activity. We suggest that the general base for the isopeptidase activity is His112 rather than Lys58. pKa calculations of these amino acids, assessed through the 1 μs molecular dynamics simulation, confirm the hypothesis. Our findings highlight the ambiguity of destabilase catalytic residues identification and build foundations for further research of structure-activity relationship of isopeptidase activity as well as structure-based protein design for potential anticoagulant drug development.

PubMed: 37095116
DOI: 10.1038/s41598-023-32459-x

Experimental method

X-RAY DIFFRACTION (1.4 Å)